Contacts of the helix formed by residues 619 - 628 (chain W) in PDB entry 5O9G
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with SER 619 (chain W).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
618W LEU* 1.3 76.9 - - - +
620W ASP* 1.3 63.1 + - - +
621W VAL* 3.4 7.7 + - - +
622W GLN* 3.8 10.8 + - - +
623W THR* 2.6 35.3 + - - -
692W MET 5.0 6.1 - - - -
693W SER 3.0 27.7 + - - -
694W SER* 4.6 4.5 - - - -
695W GLY 5.6 1.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 620 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
619W SER* 1.3 76.9 - - - +
621W VAL* 1.3 78.0 + - - +
623W THR* 3.1 7.5 + - - -
624W GLU* 2.9 33.9 + - - +
692W MET 5.6 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 621 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
619W SER* 3.4 7.3 + - - +
620W ASP* 1.3 93.6 - - - +
622W GLN* 1.3 57.0 + - - +
624W GLU* 3.2 19.0 - - - +
625W TYR* 2.9 45.3 + - + +
662W PRO* 3.6 29.8 - - + -
672W VAL* 5.0 23.8 - - + -
692W MET 5.8 0.2 - - - +
693W SER* 4.3 19.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 622 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
618W LEU* 3.8 35.5 - - + +
619W SER* 3.6 16.4 + - - +
620W ASP 3.3 0.2 - - - -
621W VAL* 1.3 76.8 - - - +
623W THR* 1.3 51.5 + - - +
625W TYR* 3.8 5.0 - - - +
626W TYR* 2.6 41.0 + - - +
658W ALA 2.8 23.8 + - - -
659W SER* 3.3 16.4 + - - +
660W ASN 3.2 9.8 - - - +
661W HIS 3.2 21.3 + - - -
662W PRO* 3.3 22.6 - - - +
693W SER 4.5 5.6 - - - +
694W SER* 3.7 4.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 623 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
618W LEU* 5.0 5.8 - - - +
619W SER 2.6 20.6 + - - -
620W ASP* 3.1 12.3 + - - -
622W GLN* 1.3 75.8 - - - +
624W GLU* 1.3 60.7 + - - +
626W TYR* 3.2 5.4 + - + +
627W LYS* 2.9 36.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 624 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
620W ASP* 2.9 17.8 + - - +
621W VAL* 3.2 31.9 - - - +
623W THR* 1.3 78.5 - - - +
625W TYR* 1.3 70.1 + - + +
627W LYS* 5.1 0.2 - - - -
628W ASN* 2.9 57.2 + - - +
629W ILE* 4.1 0.9 + - - +
671W ARG* 5.4 8.9 + - - +
672W VAL* 6.1 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 625 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
621W VAL* 2.9 44.6 + - + +
622W GLN* 3.8 5.2 - - - +
624W GLU* 1.3 88.8 - - + +
626W TYR* 1.3 56.5 + - - +
629W ILE* 3.2 37.2 - - + +
635W SER* 6.0 0.9 + - - -
655W LEU* 4.3 7.6 - - - +
658W ALA* 5.3 16.3 - - + +
662W PRO* 4.3 18.2 - - + -
665W PHE* 4.0 33.8 - + - +
667W ASN 3.0 25.8 + - - -
668W ALA* 3.4 18.2 - - + +
671W ARG* 5.7 5.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 626 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
618W LEU* 5.1 13.9 - - + -
622W GLN* 2.6 23.9 + - - +
623W THR* 3.2 6.2 + - - +
625W TYR* 1.3 79.4 - - - +
627W LYS* 1.3 69.0 + - - +
629W ILE* 4.9 2.5 - - - -
630W LEU* 5.3 10.9 - - - +
655W LEU* 5.4 16.8 - - + +
659W SER* 4.5 22.7 - - - -
823W ASP 4.9 6.1 + - - -
824W THR* 4.3 28.3 + - - -
825W VAL* 5.4 4.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 627 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
623W THR* 2.9 21.5 + - + +
626W TYR* 1.3 89.1 - - + +
628W ASN* 1.3 71.6 + - - +
629W ILE 3.2 3.2 + - - -
630W LEU* 3.6 9.6 + - - +
631W THR* 3.3 22.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 628 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
624W GLU* 2.9 44.0 + - - +
627W LYS* 1.3 81.7 - - - +
629W ILE* 1.3 62.5 + - + +
631W THR* 2.5 25.2 + - - +
633W ASN* 2.9 36.6 - - - +
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il